Seasonal transcriptome profile across three different tissues of the Andean Killifish Orestias ascotanensis

Abstract

The Andean killifish Orestias ascotanensis inhabits the high-altitude Ascotán Salt Pan, an environment with variable salinity, high UV exposure, low oxygen, and extreme daily temperature fluctuations. These conditions make it an excellent model for studying high-altitude fish biology. However, the transcriptomic responses of O. ascotanensis to seasonal acclimation remain unexplored. To investigate seasonal and tissue-specific transcriptomic profiles, RNA-seq was performed on 42 libraries from gills, skin, and muscle tissues of 14 individuals collected in summer (n = 7) and winter (n = 7). Each library had a median of 105 million reads. Principal component analysis revealed strong tissue-specific expression, and seasonal differential expression analyses identified significant transcriptomic changes within each tissue. Additionally, a bioinformatics pipeline identified 10,365 high-confidence long non-coding RNAs (lncRNAs), predicted by at least three computational tools. Compared to protein-coding genes, lncRNAs exhibited higher tissue specificity, with a predominance of monoexonic structures and shorter exon lengths. This dataset provides the first comprehensive view of seasonal mRNA and lncRNA expression in O. ascotanensis tissues.

Fig. 1

Principal component analysis (PCA) of transcriptome profiles in Orestias ascotanensis. (a) PCA of all samples, colored by tissue type (gills: red, muscle: blue, skin: green). (b) Seasonal PCA for gills (summer: light red, winter: dark red). (c) Seasonal PCA for muscle (summer: light blue, winter: dark blue). (d) Seasonal PCA for skin, showing seasonal overlap (summer: light green, winter: dark green).

Fig. 2

Tissue-specific gene expression analysis in Orestias ascotanensis. (a) UpSet plot showing the number of genes uniquely expressed or shared among gills, skin, and muscle tissues. The highest bar represents genes expressed in all tissues (13,261). (b) Venn diagram displaying the number of genes upregulated in (b) gills compared to muscle and skin (1,981 genes). (c) muscle compared to gills and skin (3,183 genes) and, (d) skin compared to gills and muscle (585).

Fig. 3

Gene ontology (GO) enrichment of tissue-enriched genes. Heatmaps of top 20 enriched terms across genes with enriched expression in. (a) gills. (b) muscle, and. (c) skin. The color gradient of the bars reflects the p-value, with darker colors representing lower p-values (higher significance). The heatmaps were produced using Metascape.

Fig. 4

Seasonal variation in Gene Ontology (GO) Terms in O. ascotanensis muscle tissue. Top 20 enriched terms for summer. (a) upregulated and (b) downregulated genes in O. ascotanensis muscle tissue. The color gradient of the bars reflects the p-value, with darker colors representing lower p-values (higher significance). The heatmaps were produced using Metascape.

Fig. 5

Workflow for the Identification and filtering of lncRNA candidates in O. ascotanensis. (a) Step-by-step process for identifying and filtering long non-coding RNA (lncRNA) candidates from the assembled transcripts of O. ascotanensis using multiple computational tools. (b) Venn diagram showing the overlap among candidate lncRNAs filtered by FEELnc, RNAmining, CPAT, and Transdecoder.

Fig. 6

Characterization of O. ascotanensis lncRNAs. (a) Density distribution of tau scores, (b) frequency distribution of the number of exons, and (c) density distribution of exon lengths for mRNAs and lncRNAs.